7NN9

NATIVE INFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Three-dimensional structure of the complex of 4-guanidino-Neu5Ac2en and influenza virus neuraminidase.

Varghese, J.N.Epa, V.C.Colman, P.M.

(1995) Protein Sci. 4: 1081-1087

  • DOI: 10.1002/pro.5560040606
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The three-dimensional X-ray structure of a complex of the potent neuraminidase inhibitor 4-guanidino-Neu5Ac2en and influenza virus neuraminidase (Subtype N9) has been obtained utilizing diffraction data to 1.8 A resolution. The interactions of the in ...

    The three-dimensional X-ray structure of a complex of the potent neuraminidase inhibitor 4-guanidino-Neu5Ac2en and influenza virus neuraminidase (Subtype N9) has been obtained utilizing diffraction data to 1.8 A resolution. The interactions of the inhibitor, solvent water molecules, and the active site residues have been accurately determined. Six water molecules bound in the native structure have been displaced by the inhibitor, and the active site residues show no significant conformational changes on binding. Sialic acid, the natural substrate, binds in a half-chair conformation that is isosteric to the inhibitor. The conformation of the inhibitor in the active site of the X-ray structure concurs with that obtained by theoretical calculations and validates the structure-based design of the inhibitor. Comparison of known high-resolution structures of neuraminidase subtypes N2, N9, and B shows good structural conservation of the active site protein atoms, but the location of the water molecules in the respective active sites is less conserved. In particular, the environment of the 4-guanidino group of the inhibitor is strongly conserved and is the basis for the antiviral action of the inhibitor across all presently known influenza strains. Differences in the solvent structure in the active site may be related to variation in the affinities of inhibitors to different subtypes of neuraminidase.


    Related Citations: 
    • Influenza Virus Neuraminidase with Hemagglutinin Activity
      Laver, W.G.,Colman, P.M.,Webster, R.G.,Hinshaw, V.S.,Air, G.M.
      (1984) Virology 137: 314
    • Gene and Protein Sequence of an Influenza Virus Neuraminidase with Hemagglutinin Activity
      Air, G.M.,Ritchie, L.R.,Laver, W.G.,Colman, P.M.
      (1985) Virology 145: 117
    • Structure of the Influenza Virus Glycoprotein Antigen Neuraminidase at 2.9 Angstroms Resolution
      Varghese, J.N.,Laver, W.G.,Colman, P.M.
      (1983) Nature 303: 35
    • The Three-Dimensional Structure of Neuraminidase of Subtype N9 from an Avian Influenza Virus
      Baker, A.T.,Varghese, J.N.,Laver, W.G.,Air, G.M.,Colman, P.M.
      (1987) Proteins 1: 111
    • The Structure of the Complex between Influenza Virus Neuraminidase and Sialic Acid, the Viral Receptor
      Varghese, J.N.,Mckimm-Breschkin, J.L.,Caldwell, J.B.,Kortt, A.A.,Colman, P.M.
      (1992) Proteins 14: 327
    • Three-Dimensional Structure of the Neuraminidase of Influenza Virus A(Slash)Tokyo(Slash)3(Slash)67 at 2.2 Angstroms Resolution
      Varghese, J.N.,Colman, P.M.
      (1991) J.Mol.Biol. 221: 473
    • Refined Atomic Structures of N9 Subtype Influenza Virus Neuraminidase and Escape Mutants
      Tulip, W.R.,Varghese, J.N.,Baker, A.T.,Van Donkelaar, A.,Laver, W.G.,Webster, R.G.,Colman, P.M.
      (1991) J.Mol.Biol. 221: 487


    Organizational Affiliation

    Biomolecular Research Institute, Parkville, Victoria, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NEURAMINIDASE N9
A
388Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9)Mutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
Find proteins for P03472 (Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9))
Go to UniProtKB:  P03472
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.152 
  • Space Group: I 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 182.800α = 90.00
b = 182.800β = 90.00
c = 182.800γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing
R-AXISdata reduction
R-AXISdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-04-03
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance